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import unittest
import datetime
from unittest import mock
import gn2.wqflask.marker_regression.run_mapping as run_mapping
from gn2.wqflask.marker_regression.run_mapping import get_genofile_samplelist
from gn2.wqflask.marker_regression.run_mapping import geno_db_exists
from gn2.wqflask.marker_regression.run_mapping import write_input_for_browser
from gn2.wqflask.marker_regression.run_mapping import export_mapping_results
from gn2.wqflask.marker_regression.run_mapping import trim_markers_for_figure
from gn2.wqflask.marker_regression.run_mapping import get_perm_strata
from gn2.wqflask.marker_regression.run_mapping import get_chr_lengths
class AttributeSetter:
def __init__(self, obj):
for k, v in obj.items():
setattr(self, k, v)
class MockGroup(AttributeSetter):
def get_genofiles(self):
return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}]
class TestRunMapping(unittest.TestCase):
def setUp(self):
self.group = MockGroup(
{"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"})
chromosomes = {
"3": AttributeSetter({
"name": "C1",
"length": "0.04"
}),
"4": AttributeSetter({
"name": "C2",
"length": "0.03"
}),
"5": AttributeSetter({
"name": "C4",
"length": "0.01"
})
}
self.dataset = AttributeSetter(
{"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"})
self.chromosomes = AttributeSetter({"chromosomes": lambda cur: chromosomes})
self.trait = AttributeSetter(
{"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"})
def tearDown(self):
self.dataset = AttributeSetter(
{"group": {"location": "~/genofiles/g1_file"}})
def test_get_genofile_samplelist(self):
results_1 = get_genofile_samplelist(self.dataset)
self.assertEqual(results_1, ["S1", "S2", "S3", "S4"])
self.group.genofile = "~/genofiles/g2_file"
result_2 = get_genofile_samplelist(self.dataset)
self.assertEqual(result_2, [])
@mock.patch("gn2.wqflask.marker_regression.run_mapping.data_set")
def test_if_geno_db_exists(self, mock_data_set):
mock_data_set.create_dataset.side_effect = [
AttributeSetter({}), Exception()]
run_mapping.create_trait = mock.Mock()
results_no_error = geno_db_exists(self.dataset, "dataset_1")
results_with_error = geno_db_exists(self.dataset, "dataset_1")
self.assertEqual(mock_data_set.create_dataset.call_count, 2)
self.assertEqual(results_with_error, "False")
self.assertEqual(results_no_error, "True")
def test_trim_markers_for_figure(self):
markers = [{
"name": "MK1",
"chr": "C1",
"cM": "1",
"Mb": "12000",
"genotypes": [],
"dominance":"TT",
"additive":"VA",
"lod_score":0.5
},
{
"name": "MK2",
"chr": "C2",
"cM": "15",
"Mb": "10000",
"genotypes": [],
"lod_score":0.7
},
{
"name": "MK1",
"chr": "C3",
"cM": "45",
"Mb": "1",
"genotypes": [],
"dominance":"Tt",
"additive":"VE",
"lod_score":1
}]
marker_2 = [{
"name": "MK1",
"chr": "C1",
"cM": "1",
"Mb": "12000",
"genotypes": [],
"dominance":"TT",
"additive":"VA",
"p_wald":4.6
}]
results = trim_markers_for_figure(markers)
result_2 = trim_markers_for_figure(marker_2)
expected = [
{
"name": "MK1",
"chr": "C1",
"cM": "1",
"Mb": "12000",
"genotypes": [],
"dominance":"TT",
"additive":"VA",
"lod_score":0.5
},
{
"name": "MK1",
"chr": "C3",
"cM": "45",
"Mb": "1",
"genotypes": [],
"dominance":"Tt",
"additive":"VE",
"lod_score":1
}
]
self.assertEqual(results, expected)
self.assertEqual(result_2, marker_2)
def test_export_mapping_results(self):
"""test for exporting mapping results"""
datetime_mock = mock.Mock(wraps=datetime.datetime)
datetime_mock.now.return_value = datetime.datetime(
2019, 9, 1, 10, 12, 12)
markers = [{
"name": "MK1",
"chr": "C1",
"cM": "1",
"Mb": "12000",
"genotypes": [],
"dominance":"TT",
"additive":"VA",
"lod_score":3
},
{
"name": "MK2",
"chr": "C2",
"cM": "15",
"Mb": "10000",
"genotypes": [],
"lod_score":7
},
{
"name": "MK1",
"chr": "C3",
"cM": "45",
"Mb": "1",
"genotypes": [],
"dominance":"Tt",
"additive":"VE",
"lod_score":7
}]
with mock.patch("builtins.open", mock.mock_open()) as mock_open:
with mock.patch("gn2.wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
results_path="~/results", mapping_method="gemma", mapping_scale="physic",
score_type="-logP", transform="qnorm",
covariates="Dataset1:Trait1,Dataset2:Trait2",
n_samples="100", vals_hash="")
write_calls = [
mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
mock.call('Population: Human GP1_\n'), mock.call(
'Data Set: dataset_1\n'),
mock.call('Trait: Test Name\n'),
mock.call('Trait Hash: \n'),
mock.call('N Samples: 100\n'),
mock.call('Mapping Tool: gemma\n'),
mock.call('Transform - Quantile Normalized\n'),
mock.call('Gene Symbol: IGFI\n'), mock.call(
'Location: X1 @ 123313 Mb\n'),
mock.call('Cofactors (dataset - trait):\n'),
mock.call('Trait1 - Dataset1\n'),
mock.call('Trait2 - Dataset2\n'),
mock.call('\n'), mock.call('Name,Chr,'),
mock.call('Mb,-logP'),
mock.call(',Additive'), mock.call(',Dominance'),
mock.call('\n'), mock.call('MK1,C1,'),
mock.call('12000,'), mock.call('3'),
mock.call(',VA'), mock.call(',TT'),
mock.call('\n'), mock.call('MK2,C2,'),
mock.call('10000,'), mock.call('7'),
mock.call('\n'), mock.call('MK1,C3,'),
mock.call('1,'), mock.call('7'),
mock.call(',VE'), mock.call(',Tt')
]
mock_open.assert_called_once_with("~/results", "w+")
filehandler = mock_open()
filehandler.write.assert_has_calls(write_calls)
@mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice")
def test_write_input_for_browser(self, mock_choice):
"""test for writing input for browser"""
mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"]
with mock.patch("builtins.open", mock.mock_open()) as mock_open:
expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT']
results = write_input_for_browser(
this_dataset=self.dataset, gwas_results={}, annotations={})
self.assertEqual(results, expected)
def test_get_perm_strata(self):
categorical_vars = ["C1", "C2", "W1"]
used_samples = ["S1", "S2"]
sample_list = AttributeSetter({"sample_attribute_values": {
"S1": {
"c1": "c1_value",
"c2": "c2_value",
"w1": "w1_value"
},
"S2": {
"w1": "w2_value",
"w2": "w2_value"
},
"S3": {
"c1": "c1_value",
"c2": "c2_value"
},
}})
results = get_perm_strata(this_trait={}, sample_list=sample_list,
categorical_vars=categorical_vars, used_samples=used_samples)
self.assertEqual(results, [1, 1])
def test_get_chr_length(self):
"""test for getting chromosome length"""
cursor = mock.MagicMock()
chromosomes = AttributeSetter({"chromosomes": self.chromosomes})
dataset = AttributeSetter({"species": chromosomes})
results = get_chr_lengths(
mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[])
chr_lengths = []
for key, chromo in self.chromosomes.chromosomes(cursor).items():
chr_lengths.append({"chr": chromo.name, "size": chromo.length})
self.assertEqual(chr_lengths, results)
qtl_results = [{
"chr": "16",
"cM": "0.2"
},
{
"chr": "12",
"cM": "0.5"
},
{
"chr": "18",
"cM": "0.1"
},
{
"chr": "22",
"cM": "0.4"
},
]
result_with_other_mapping_scale = get_chr_lengths(
mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results)
expected_value = [{'chr': '1', 'size': '0'}, {
'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}]
self.assertEqual(result_with_other_mapping_scale, expected_value)
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